A good way to improve performance is to remove as much as possible the calls to the "allInstances" operation if there are some (they can often be replaced by specific navigation inside the input model).
Also, you have to double-check the complexity of your OCL expressions: e.g. doing an appropriate use of the "select" operation can save quite a lot of time.

However, depending on the elements actually handled by the transformation, it could be normal that the execution time (reasonably) increases when augmenting the size of the input models.